5M1Y

The case of 1lkr held at the PDB and its variable amino acid occupancies; re refinement of 4ow9 to correct this

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus
  • Mutation(s): No 

  • Deposited: 2016-10-11 Released: 2016-10-26 
  • Deposition Author(s): Helliwell, J.R.
  • Funding Organization(s): Engineering and Physical Sciences Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The case of 1lkr held at the PDB and its variable amino acid occupancies; re refinement of 4ow9 to correct this

Helliwell, J.R.Tanley, S.W.M.

(2016) Zenodo 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA, B129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], Z [auth B]PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , CA [auth B] , DA [auth B] , E [auth A] , EA [auth B] , F [auth A] , FA [auth B] , 
AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
HA [auth B], IA [auth B], JA [auth B], P [auth A], Q [auth A], R [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
KA [auth B], S [auth A], T [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
LA [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.251α = 90
b = 62.537β = 90.92
c = 58.981γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-10-11 
  • Released Date: 2016-10-26 
  • Deposition Author(s): Helliwell, J.R.
  • This entry supersedes: 4OW9

Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations